I'm testing a box that someone else has setup and I managed to get into the FTP server on it and then download the .htpasswd file. When opened it had a user:hash in it and then I put that in a txt file and then ran John The Ripper on it.

It took about 23 minutes and it came up with the password. However, if I try to use that account on ftp or even RDP it won't work. Is there a chance that somehow it got it wrong with JTR? Also, this is a Windows box running this...

That's used for password-protecting web access. Can you authenticate to the password protected area(s) of the website? There's always a chance credentials could be reused with other services, but they're not going to use that file as a credential store.